Bases Affecting Duplex Stability

The stability of DNA duplexes is dependent on a complex array of hydrogen bonding among amino and carbonyl groups of the heteroaromatic bases and surrounding water molecules, as well as base stacking interactions. The heteroaromaticity of the bases with their inherent dipole moments leads to base stacking interactions, which are electrostatic and hydrophobic in nature. The intermolecular interactions affecting base stacking may be inter strand or intra strand. A common strategy to modify duplex stability is to focus on modification of the nucleobases.